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Classifier training

Supplementary Figure 1. DIGE analysis. Cluster analysis. ELISA assays. Prediction analysis (LDA). 1. 3. 2. Predictor discovery in training set. Predictor test in testing set. DIGE raw gel images Matched samples SJIA (10 F, 10 Q) POLY (5 F, 5 Q). 2d hierarchical clustering

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Classifier training

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  1. Supplementary Figure 1 DIGE analysis Cluster analysis ELISA assays Prediction analysis (LDA) 1 3 2 Predictor discovery in training set Predictor test in testing set DIGE raw gel images Matched samples SJIA (10 F, 10 Q) POLY (5 F, 5 Q) 2d hierarchical clustering heatmap plotting 12 ELISA Assay development 4 5 7 Test to anticipate SJIA F in Q randomization Training set SJIA (12 F, 12 Q) Testing set SJIA (10 F, 10 Q) ELISA assay FI (27 ) KD (10) SJIA F(12) FI (15) 9 FDR analysis ELISA assay Q->F (5) Q->Q (10) Feature selection Spot finding spot alignment feature extraction 15 protein 2d clustering LDA Fisher exact test Normalization manual review Classifier training Blind testing Classifier training 7 ELISA assay Clustering Box-and-Whisker Analysis Fisher exact test Fisher exact test Manual review Discriminate SJIA F SJIA Q POLY F POLY Q Discriminate SJIA F KD FI Classify SJIA F vs Q Classify SJIA F vs Q Classify SJIA F vs FI MSMS Protein ID

  2. Supplementary Figure 2 A B Patient 1 and Patient 2 whole plasma 3 2 4 1 5 Removed proteins: 1 anti-trypsin 2 albumin 3 serrotransferrin 4 Ig heavy chain 5 Haptoglobin 6 Ig light chain 6 MW/1000 Patient 1 and Patient 2 after protein depletion 3 2 4 1 5 Hemoglobin 6 pH

  3. SJIA F Q C3 AGP1 ACT SAP SAA S100A8 S100A9 HP CRP C9 C4 APO-IV APO-L1 AMBP KLKB1 VDB CFH ATIII A2M ATIII APO-E APO-D FGG FGB TTR GSN APOA1 Figure 1

  4. POLY F Q SJIA SJIA SJIA A B F Q F KD F FI 0.30 0.25 TTR CFH 0.20 APO A1 A2M GSN False discovery rate (FDR) 0.15 C4 AGP1 ACT 0.10 APO IV SAP HP 0.05 CRP S100A8 S100A9 0.00 SAA 20 1 2 5 10 Number of features called significant P value: 1.1 E -4 P value: 0.5 P value: 0.19 P value: 1.4 E -4 Figure 2

  5. Goodness of class separation – D probability SJIA Training SJIA Test Feature# 4 5 6 7 8 9 12 4 5 6 7 8 9 12 Figure 3

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